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DESCRIPTION
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DESCRIPTION
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Package: HemaScopeR
Type: Package
Title: HemaScopeR: A Specialized Bioinformatics Toolkit Designed for Analyzing both Single-cell and Spatial Transcriptome Sequencing Data from Hematopoietic Cells
Version: 1.0.0
Author: Zhenyi Wang <[email protected]> and Yuxin Miao <[email protected]>
Maintainer: Zhenyi Wang <[email protected]> and Yuxin Miao <[email protected]>
Description: HemaScopeR, a specialized bioinformatics toolkit designed for comprehensive analysis of
scRNA-seq and st-seq data derived from hematopoietic cells, including those from myeloid and lymphoid lineages.
Depends: R (>= 4.2), shiny, textshaping, shinyjs, Seurat, phateR, DoubletFinder, monocle, slingshot, GSVA,
limma,plyr,dplyr,org.Mm.eg.db,org.Hs.eg.db,CellChat,velocyto.R,SeuratWrappers,stringr,scran,ggpubr,
viridis, pheatmap, parallel, reticulate, SCENIC, feather, AUCell, RcisTarget, Matrix, foreach, doParallel,
clusterProfiler, RColorBrewer, Rfast2, SeuratDisk, abcCellmap, biomaRt, copykat, gelnet, ggplot2,
parallelDist, patchwork, markdown
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Collate:
'OpenXGR_oDefineNet.r'
'OpenXGR_oGGnetwork.r'
'OpenXGR_oLayout.r'
'OpenXGR_oNetInduce.r'
'OpenXGR_oSubneterGenes.r'
'main_st_10x_visium_pipeline.R'
'sc_10x_chromium_mainPipeline.R'
'sc_Step10_calculate_lineage_scores.R'
'sc_Step11_run_GSVA.R'
'sc_Step12_prepareDataForScvelo.R'
'sc_Step12_run_monocle.R'
'sc_Step12_run_slingshot.R'
'sc_Step13_run_SCENIC.R'
'sc_Step14_run_CellChat.R'
'sc_Step2_QC_multiple_scRNASeq.R'
'sc_Step2_QC_single_scRNASeq.R'
'sc_Step4_CNV_analysis.R'
'sc_Step4_cellAnnotation.R'
'sc_Step4_query_data.R'
'sc_Step5_run_phateR.R'
'sc_Step7_assign_cell_cycle.R'
'sc_Step8_heterogeneity.R'
'sc_Step9_violin_plot_for_marker_genes.R'
'sc_assistantFunctions.R'
'sc_doublerFinderwraper.R'
'shiny_Server_main.R'
'shiny_UI_main.R'
'shiny_sc_step10_fluidRow.R'
'shiny_sc_step11_fluidRow.R'
'shiny_sc_step12_fluidRow.R'
'shiny_sc_step13_fluidRow.R'
'shiny_sc_step14_fluidRow.R'
'shiny_sc_step15_fluidRow .R'
'shiny_sc_step1_fluidRow.R'
'shiny_sc_step2_fluidRow.R'
'shiny_sc_step3_fluidRow.R'
'shiny_sc_step4_fluidRow.R'
'shiny_sc_step5_fluidRow.R'
'shiny_sc_step6_fluidRow.R'
'shiny_sc_step7_fluidRow.R'
'shiny_sc_step8_fluidRow.R'
'shiny_sc_step9_fluidRow.R'
'shiny_st_step10_fluidRow.R'
'shiny_st_step11_fluidRow.R'
'shiny_st_step1_fluidRow.R'
'shiny_st_step2_fluidRow.R'
'shiny_st_step3_fluidRow.R'
'shiny_st_step4_fluidRow.R'
'shiny_st_step5_fluidRow.R'
'shiny_st_step6_fluidRow.R'
'shiny_st_step7_fluidRow.R'
'shiny_st_step8_fluidRow.R'
'shiny_st_step9_fluidRow.R'
'st_10x_visium_mainPipeline.R'
'st_Step10_NicheAnalysis.R'
'st_Step1_Loading_Data.R'
'st_Step2_QC_spatial.R'
'st_Step3_Clustering.R'
'st_Step4_Find_DEGs.R'
'st_Step5_SpatiallyVariableFeatures.R'
'st_Step6_Interaction.R'
'st_Step7_CNV_analysis.R'
'st_Step8_Deconvolution.R'
'st_Step9_Cellcycle.R'
'st_assistantFunctions.R'